BMTools
Project description
bmtools
A collection of scripts to make developing networks in BMTK easier.
Getting Started
Installation
pip install bmtool
For developers who will be pulling down additional updates to this repository regularly use the following instead.
git clone https://github.com/tjbanks/bmtools
cd bmtools
python setup.py develop
Then download updates (from this directory) with
git pull
Example Use
> cd your_bmtk_model_directory
> bmtools
Usage: bmtools [OPTIONS] COMMAND [ARGS]...
Options:
--verbose Verbose printing
--help Show this message and exit.
Commands:
debug
plot
util
>
> bmtools plot
Usage: bmtools plot [OPTIONS] COMMAND [ARGS]...
Options:
--config PATH Configuration file to use, default: "simulation_config.json"
--no-display When set there will be no plot displayed, useful for saving
plots
--help Show this message and exit.
Commands:
connection Display information related to neuron connections
positions Plot cell positions for a given set of populations
raster Plot the spike raster for a given population
report Plot the specified report using BMTK's default report plotter
>
> bmtools plot positions
Single Cell Tuning
From a BMTK Model directory containing a simulation_config.json
file:
bmtools util cell tune --builder
For non-BMTK cell tuning:
bmtools util cell --template TemplateFile.hoc --mod-folder ./ tune --builder
FIR Curve plotting
> bmtools util cell fir --help
Usage: bmtools util cell fir [OPTIONS]
Creates a NEURON GUI window with FI curve and passive properties
Options:
--title TEXT
--min-pa INTEGER Min pA for injection
--max-pa INTEGER Max pA for injection
--increment FLOAT Increment the injection by [i] pA
--tstart INTEGER Injection start time
--tdur INTEGER Duration of injection default:1000ms
--advanced Interactive dialog to select injection and recording
points
--help Show this message and exit.
> bmtools util cell fir
? Select a cell: (Use arrow keys)
» CA3PyramidalCell
DGCell
IzhiCell
IzhiCell_BC
IzhiCell_EC
IzhiCell_EC2
IzhiCell_EC_BIO
IzhiCell_EmoExcitatory
IzhiCell_EmoInhibitory
IzhiCell_OLM
IzhiCell_int
Planned future features
bmtools build
Create a starting point network
Download sample networks
bmtools plot
Plot variable traces
Plot spike rasters
X Plot cell positions
X Plot connection matricies
bmtools debug
X list cell types available for single debug
X Run a single cell in the network
Isolate a single cell in the network
Project details
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